DNA methylation constitutes the most stable type of epigenetic modifications modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation reference profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of 6 annotation categories, revealed evolutionary conserved regions to be the predominant sites for differential DNA methylation and a core region surrounding the transcriptional start site as informative surrogate for promoter methylation. We find 17% of the 873 analyzed genes differentially methylated in their 5′-untranslated regions (5′-UTR) and about one third of the differentially methylated 5′-UTRs to be inversely correlated with transcription. While our study was controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought.

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine–guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data.

6] S. Pasynkiewicz, Po/i./idron 1990. 9. 429. 171 Crystal data of [3(thf),] 6 T H F M = 1986.46, rhomhohedral, space group R k . [I = h = 2353.6(3). c = 3133.0(6) pm. Y = 15.030(4) nm'. Z = 6. pL,,,Cd = 1.317 Mgm-3. F(000) = 6264. ; . =71.073 pm, T = -120 C . p(MoK,) = 1.651 mni-'. crystal dimensions: 0.7 x0.5 xO.5 mm, 6 5 2 0 < 40 ; of the 6127 collected reflections, 2440 are independent, and these were used for the refinement of 164 parameters with the help of 198 restraints: maximal residual electron density: 899 enin-'. R I ( F > 4 o ( F ) ) = 0.069 and wR2 = 0.199 (all data) with R1 = X l l F , l ~ ~k :~~, I~F o \ and PIRZ = (Zii,F~:-Ff)*:Zii.(F3)l)il '.The data here collected on a Stoe-Huher diffractometer. Intensities of 3 rapidlq cooled crgstiil in a n oil drop [XI Mere collected by 2 0 :~ method. Semiempirical absorption corrections were carried out on all data. The structure was solved hg direct methods (SHELXS-90) [9] and refined by least squares on F' [lo]. The disorders of the T H F solvent molecules were refined with dictance restraints. The refinement of the inversion twinning paramter 11 I ] ( \ = 0.00 (4) for .r = 0 for the correct absolute structure and i = + 1 for the inverted structure) confirmed the absolute structure of3. The solution of the structure and the refinement in the space group R5c were unsuccessful. The structure could he solved in the space group C<,, but a refinement was also here unsuccessful. Further details of the crystal structure investigation may he obtained from the Director of the Cambridge Crystallographic Data Centre. 12 Union Road, GB-Cambridge CB2 IEZ. on quoting the full journal citation. 1i5. 4971. An,qew. Chon. Inr. E d Engl. 1994, 33. No. 12 VCH Yerluxsgrsellschufr mhH, 0-69451 Weinherni, 1994 0570-0833,'94!1212-1?47 J 10.00 + .2SW

Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation occurs in a tumour type-specific manner. However, large-scale analysis of candidate genes has so far been hampered by the lack of high throughput assays for methylation detection. We have developed the first microarray-based technique which allows genome-wide assessment of selected CpG dinucleotides as well as quantification of methylation at each site. Several hundred CpG sites were screened in 76 samples from four different human tumour types and corresponding healthy controls. Discriminative CpG dinucleotides were identified for different tissue type distinctions and used to predict the tumour class of as yet unknown samples with high accuracy using machine learning techniques. Some CpG dinucleotides correlate with progression to malignancy, whereas others are methylated in a tissue-specific manner independent of malignancy. Our results demonstrate that genome-wide analysis of methylation patterns combined with supervised and unsupervised machine learning techniques constitute a powerful novel tool to classify human cancers.

As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of methylation can have severe consequences. An accurate quantification of the methylation status at any given position of the genome is a powerful diagnostic indicator. Here we present the first assay for the analysis and precise quantification of methylation on CpG positions in simplex and multiplex reactions based on matrix-assisted laser desorption/ ionisation mass spectrometry detection. Calibration curves for CpGs in two genes were established and an algorithm was developed to account for systematic fluctuations. Regression analysis gave R(2) >or= 0.99 and standard deviation around 2% for the different positions. The limit of detection was approximately 5% for the minor isomer. Calibrations showed no significant differences when carried out as simplex or multiplex analyses. All variable parameters were thoroughly investigated, several paraffin-embedded tissue biopsies were analysed and results were verified by established methods like analysis of cloned material. Mass spectrometric results were also compared to chip hybridisation.